Members of the AraC protein family regulate a broad range of activities important in the pathogenicity of E. coli: bacterial stress response, invasion of intestinal mucosa and toxin release. The proteins MarA and SoxS (approximately 45% identical to MarA), members of the AraC family, are transcriptional activators that mediate resistance to superoxides, organic solvents and a broad range of antibiotics in a number of gram-negative bacteria. How MarA and SoxS bind DNA and activate transcription is unknown. In collaboration with S. Rhee, D. Davies and J. L. Rosner, the structure of MarA bound to a cognate DNA oligonucleotide (marbox) has been solved by X-ray crystallography. MarA binds the DNA as a monomer by virtue of two helix-turn-helix (HTH) motifs organized about a hydrophobic core. Numerous contacts between the recognition helices and the DNA major groove and overall shape complementarity between MarA and DNA provide for the somewhat loose sequence-specificity. MarA and SoxS activate the same target genes but to different extents. Activation involves recognition by the activator of a highly degenerate marbox sequence that can be centered at various positions upstream of the site of RNA polymerase (RNP) binding. In contrast to most bacterial transcriptional activators which act as dimers and recognize symmetrical binding sites, we (J. L. Rosner & W. Gillette) find that the marbox is asymmetrical: it is functional in one orientation when centered at less than 55 base pairs upstream of the transcriptional start site but functions in the other orientation when the marbox is farther upstream. We also find that the differential activation of a particular promoter by MarA or SoxS is primarily dependent on the marbox sequence rather than on the downstream portion of the promoter. In vitro, the difference between MarA and SoxS transcriptional activation seems to parallel their binding energies for the formation of activator-RNP-DNA triple complexes. A major problem for the solution of nucleotide structures by NMR spectroscopy has been the availability of C-14 and N-15 substituted nucleotides. In collaboration with J. L. Louis, G. M. Clore and A. M. Gronenborn we have devised a simple technique for the synthesis of uniformly isotope-labeled DNA oligonucleotides.